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IDrawVisitor interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing.IFontManager interface.IGeneratorParameter implementations.IChemObjects.TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
TextElement into widget specific objects.
IChemObject can be read or written.
IChemObject can be read or written.
IChemObject can be read or written.
IChemObject can be read or written.
AcidicGroupCountDescriptor.
IMonomer or a Strand.
IMonomer or a Strand.
IChemObjectIOListener to this IChemObjectIO.
IChemSequence to this container.
IRenderingElement for linear arrows.IAtomContainer classes.IAtomContainers.IAtom classes.atomIndex.
atom.
atomIndex and with a
maximum height of height.
atom and with a
maximum height of height.
atomIndex, with maximum
height of height, and using a particular invariant type.
atom, with maximum
height of height, and using a particular invariant type.
IAtomType classes.IDifference between two IAtomType.Hybridizations.AtomType class.AtomTypeMapper allows the mapping of atom types between atom type
schemes.IDrawVisitor interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing.IDrawVisitor using the AWT widget toolkit,
taking a Graphics2D object to which the chemical content
is drawn.
IRenderingElements for atoms in an atom container.IAtomColorer used to draw elements.BasicAtomGenerator.CompactAtom parameter.BasicGroupCountDescriptor.
Sets, where each set contains all edge that are
in the same biconnected component.
IBond classes.IDifference between two IBond.Orders.IBonds.IDifference between two Booleans.RGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph.
Atom atom in the environment
of the atoms in the AtomContainer.
IMolecule.
IAtomContainer.
IAtomContainer.
IAtomContainer.
IAtomContainer.
IAtomContainer.
IAtomContainer.
AtomContainer.
IAtomContainer.
IAtomContainer.
AtomContainer.
AtomContainer.
IAtomContainer.
VABCVolume class.
IAtomContainer.
IChemObject, calculates the bounding rectangle in screen
space.
IChemObject, calculates the bounding rectangle in screen
space.
RDF.org/openscience/cdk/dict/data/cdk-atom-types.owl.org.openscience.cdk.smsd.algorithm.cdk.CDKMCS.org.openscience.cdk.smsd.algorithm.cdk.CDKMCS.ILigand is different from the previous
one according to the CIPLigandRule.
IChemObject classes.IDifference between two IChemObjects.Iterable to ChemSequences of this container.
ILigands based on CIP sequences sub rules.ChemModel and its content.
IChemObject.
Mapping and the mapped IChemObjects.
Reaction and its content.
ReactionSet and the contained Reactions
too.
RingSet including the Rings.
ChemModel and its content.
IChemObject.
Mapping and the mapped IChemObjects.
Reaction and its content.
ReactionSet and the contained Reactions
too.
RingSet including the Rings.
IMoleculeSet or a IMolecule object to CML 2 code.LoggingTool to configurate the Log4J toolkit.
IChemObject is part of the current selection.
IChemObject into RDF using a
Jena model and the CDK data model ontology.LoggingTool for the given class.
SystemOutLoggingTool for the given class.
molecule.
ILoggingTool for the given
sourceClass.
molecule.
Reaction.
molecule.
molecule.
Serializer with the sole purpose and functionality to not
output the XML declaration.CustomSerializer using the matching
Serializer.Serializer(OutputStream).
CustomSerializer using the matching
Serializer.Serializer(OutputStream, String).
IChemObject for the original CDK
implementation.AllRingsFinder.
ICDKObject for the original CDK
implementation.IRandomAccessChemObjectReader's can implement to
have it take care of basic stuff, like managing the ReaderListeners.IAtomContainer.
IAtomContainer.
IBond.Order to a numeric value.
IAtomContainer.
IDifference between two Double.IChemObject classes.IElement classes.Collection of all selected IChemObjects of the
given type.
IAtomContainer, that
extends the Fingerprinter with additional bits describing ring
features.DEFAULT_SIZE
and with a search depth of DEFAULT_SEARCH_DEPTH.
AllRingsFinder.findAllRings(IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes)
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes)
DEFAULT_SIZE
and with a search depth of DEFAULT_SEARCH_DEPTH.
MM2BasedParameterSetReader.IChemObject from the chemical data model into
something that can be drawn in the chemical drawing.
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing.
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing.
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing.
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing.
IRenderingElements grouped
together into a tree.
IGeneratorParameter for the active IRenderer.
Atoms in the
AtomContainer for the 2D coordinates.
Atoms in the
AtomContainer for the 2D coordinates.
number in [0,..].
number in [0,..].
number in [0,..].
number in the
container.
IAtomContainer of which this ligand is part.
IAtomContainer of which this ligand is part.
number in the
container.
number in the
container.
Map with atom type mappings.
BitSet (which's size = number of bond
in the atomContainer, all the bit are set to true).
number in [0,..].
number in [0,..].
number in [0,..].
AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
IChemObjectBuilder for the data classes that extend
this class.
IAtom to which this ligand is connected via one IBond.
IAtom to which this ligand is connected via one IBond.
number in the
container.
number in the
container.
number in the
container.
number in the container.
number in the container.
number in the container.
IGeneratorParameter for the
active IRenderer.
IReaction.Direction of the reaction.
number in the
container.
number in the
container.
number in the
container.
IFontManager interface.
IResourceFormat class for this IO class.
IResourceFormat class for this IO class.
IResourceFormat for this reader.
IResourceFormat for this writer.
IAtomContainer objects..
IAtomContainer objects.
IAtomContainer objects.
IAtomContainer as objects.
List of IGenerators for this renderer.
List of IGenerators for this renderer.
root in the IAtomContainer ac.
root in the IAtomContainer ac.
IAtomContainer.
InChIGeneratorFactory instance,
if needed also creates it.
IOSettings defined by this IChemObjectIO class.
IAtom of the ligand that is connected to the central IAtom via
one IBond.
IAtom of the ligand that is connected to the chiral IAtom via
one IBond.
ILoggingTool implementation.
number in [0,..].
number in [0,..].
number in [0,..].
number in the
chemObject.
number in the
chemObject.
number in the
chemObject.
number in the
chemObject.
number in the
chemObject.
number in the
container.
number in the
container.
number in the
container.
Monomer object by specifying its name.
Monomers in this
BioPolymer.
Monomers in this
BioPolymer.
Monomers in this
polymer.
Monomers in this
polymer.
Monomers in this
polymer.
Monomers in this
BioPolymer.
Monomers in this
polymer.
Monomers in this
polymer.
Monomers in this
polymer.
number in the
container.
number in the
container.
number in the
container.
IGeneratorParameter for the active IRenderer.
IGeneratorParameter for this particular
generator.
IGeneratorParameter for this particular
generator.
IGeneratorParameter for this particular
generator.
IGeneratorParameter for this particular
generator.
IGeneratorParameter for this particular
generator.
IGeneratorParameter for this particular
generator.
number in the
container.
number in the
container.
number in the
container.
RendererModel used by this renderer, which provides
access to the various parameters used to generate and draw the diagram.
IGeneratorParameters for the current
RendererModel.
IAtomContainer objects.
IChemObjectSelection with the currently selected
IChemObjects.
number in [0,..].
number in [0,..].
number in [0,..].
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
DescriptorSpecification which specifies which descriptor is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which descriptor
is implemented by this class.
Map which specifies which reaction
is implemented by this class.
Strands in this
BioPolymer.
Strands in this
BioPolymer.
Strands in this
BioPolymer.
InChITautomerGenerator.getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already
provided as input argument.
Fingerprinter which does not take bond orders
into account.defaultSize
and with a search depth of defaultSearchDepth.
IChemObject reader
for this file format.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReader.
IChemObjectReader.
IChemObjectReader.
IChemObjectReader.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IChemObjectReaderErrorHandler.
IGeneratorParameters has been
registered.
IAtomContainer.DEFAULT_SIZE
and with a search depth of DEFAULT_SEARCH_DEPTH.
IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.IChemObject containing a number of ChemSequences.ICDKObject instance for a specific
implementation.IChemObjectReader errors.IAtomContainer or
IChemModel.Objects.IDifference between two Objects which contains one or more child
IDifference objects.IDrawVisitor is an IRenderingVisitor that can be
customized and knows about fonts and other rendering parameters.IGenerator converts chemical entities into parts of the
chemical drawing expressed as IRenderingElements.IMolecule objects.Ligand to which no further recursion must be applied.InChIGenerator and InChIToStructure.IDifference between two Integer.IAtomContainers.IAtom's.ListIterator.RDFCalculator.IRenderingVisitor is responsible of converting an abstract
chemical drawing into a widget set specific drawing.ring in the molecule for aromaticity.
IAtomContainer is connected.
Algorithm types:
IIsotope classes.input.
Iterable for looping over all isotopes in this IMolecularFormula.
atom1 and atom2 share membership in the same ring or ring system.
Object.
ILoggingTool.ILonePair classes.atom matches this IQueryAtom.
bond matches this IQueryBond.
IMolecule
to the MDL molfile format.
IMolecule
to a given OutputStream.
Model into an IMolecule using the given IChemObjectBuilder.
IMolecularFormula's.IMolecule into a Model representation using the CDK OWL.
AtomSignatures and to get
the canonical [Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules
Using Extended Valence Sequences, Journal of Chemical Information and Computer
Sciences, 2004, 44:427-436] signature string for a molecule.height
for molecule molecule.
Reader.
InputStream.
ICDKObject, using the constructor defined by the
given parameters.
IChemObject for the original CDK
implementation.ILigand objects in the array according to the CIP rules.
Resource matching the given IBond.Order.
IQueryBond that matches IBond object only based on bond order, and
disregarding any aromaticity flag.OWLAtomTypeReader.OWLAtomTypeMappingReader.OWLBasedAtomTypeConfigurator.OWLBasedAtomTypeConfigurator.QueryAtomContainer
IPDBAtom from a String containing an element symbol.
IPDBAtom from an Element and a Point3d.
IPDBAtom from a String containing an element symbol.
IPDBAtom from an Element and a Point3d.
IMonomers.
IMonomers.
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher.
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher.
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher.
IAtoms in the
IAtomContainer, using the CDKAtomTypeMatcher.
size.
RingPlacer.defaultAngles.
RMap on a molecule.
0 or 1.
0 and 1.
0 and 1.
0 and 1.
0 and 1.
Iterable over Reactions of this container.
IMoleculeSet from the input source.
IGenerators
with this model.
Iterable to the two IChemObjects.
IChemObjectIOListener from this IChemObjectIO.
IRenderer that contains settings for drawing objects.Resource object into the matching IBond.Order.
RGroupList.RGroupQuery.IRGroupQuery
to the Symx RGFile format.
IAtomContainer coordinates by the rotation matrix.
Writer.
OutputStream.
RGraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
IGeneratorParameter for the active IRenderer.
number in [0,..].
number in [0,..].
number in [0,..].
Atoms in the given container.
Descriptor objects.
DescriptorSpecification objects.
IFontManager this IDrawVisitor should use.
ILoggingTool implementation to be used.
IDescriptor does not have any parameters.
long seed.
RendererModel this IDrawVisitor should use.
RendererModel this IDrawVisitor should use.
IChemObject.
IChemObjects.
debug(Throwable).
debug(Throwable).
debug(Throwable).
IChemObject
matching this IRenderer implementation.
IChemObject, but preserves references to Objects.
IChemObject, but preserves references to Objects.
height.
ICDKObject for the original CDK
implementation.CycleBasis.ISingleElectron classes.SingleMapping).crossover is using SPLIT_MODE_BREADTH_FIRST mode.
crossover is using SPLIT_MODE_DEPTH_FIRST mode.
crossover is using SPLIT_MODE_RADNDOM mode.
IDifference between two String.IFingerprinter that gives a bit set which has a size equal to the number
of substructures it was constructed from.StandardSubstructureSets.
ILoggingTool interface that sends output to
the System.out channel.text to be
drawn at position (x,y) in the color color.
VABCVolume class.VASPReader instance.
IRenderingElement into a widget toolkit specific
rendering element.
IRenderingElement into a widget toolkit specific
rendering element.
visitedAtoms list to the current
list.
CIPTool to keep track of which atoms have
already been visited.IAtoms.
IChemObject to the MDL molfile formated output.
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